chr15-74720599-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001319217.2(CYP1A1):c.1429C>T(p.Arg477Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,614,076 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001319217.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP1A1 | NM_001319217.2 | c.1429C>T | p.Arg477Trp | missense_variant | 7/7 | ENST00000379727.8 | |
CYP1A1 | NM_000499.5 | c.1429C>T | p.Arg477Trp | missense_variant | 7/7 | ||
CYP1A1 | NM_001319216.2 | c.1342C>T | p.Arg448Trp | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP1A1 | ENST00000379727.8 | c.1429C>T | p.Arg477Trp | missense_variant | 7/7 | 1 | NM_001319217.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000519 AC: 79AN: 152182Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251266Hom.: 1 AF XY: 0.000140 AC XY: 19AN XY: 135798
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461776Hom.: 1 Cov.: 30 AF XY: 0.000109 AC XY: 79AN XY: 727198
GnomAD4 genome ? AF: 0.000519 AC: 79AN: 152300Hom.: 1 Cov.: 32 AF XY: 0.000577 AC XY: 43AN XY: 74476
ClinVar
Submissions by phenotype
CYP1A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 23, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at